Recent advances in oligonucleotide probe-based technologies have employed changes in fluorescence quenching and probes or primers comprising intramolecularly base-paired secondary structures for detection of nucleic acid target sequences. In these systems, a donor fluorophore and a quencher dye are in close proximity in the intramolecularly base-paired secondary structure in the absence of the target sequence but become spatially separated in the presence of target due to unfolding of the secondary structure. The separation of the two dyes reduces quenching of the donor fluorophore which may be detected as an increase in donor fluorescence. This indicates that the target is present and/or is being amplified. That is, the donor and acceptor are linked to a single, intramolecularly base-paired oligonucleotide such that there is a detectable difference in the fluorescence properties of one or both when the oligonucleotide is unhybridized vs. when it is hybridized to its complementary sequence. For example, a self-complementary oligonucleotide labeled at each end may form a hairpin which brings the two fluorophores (i.e., the 5' and 3' ends) into close proximity where energy transfer and quenching can occur. Hybridization of the self-complementary oligonucleotide to its complement on a second oligonucleotide disrupts the hairpin and increases the distance between the two dyes, thus reducing quenching. Hairpin structures labeled in this manner are described by Tyagi and Kramer (1996. Nature Biotech. 14, 303-308) and B. Bagwell, et al. (1994. Nucl. Acids Res. 22, 2424-2425; U.S. Pat. No. 5,607,834). In contrast, the secondary structure-containing detector oligonucleotides disclosed in U.S. Pat. No. 5,928,869 have the target binding sequence wholly or partially in a single-stranded "tail" region rather than fully contained within the intramolecularly base-paired secondary structure. The secondary structure (e.g., a hairpin) therefore need not unfold in order to initially hybridize to the target. Hybridization of the single-stranded tail is not competitive so the kinetics of the reaction favor hybridization to the target.